HEADER SIGNALING PROTEIN 28-APR-13 4KFV TITLE STRUCTURAL INSIGHT INTO GOLGI MEMBRANE STACKING BY GRASP65 AND GRASP55 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GOLGI REASSEMBLY-STACKING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 12-210; COMPND 5 SYNONYM: GORASP1 PROTEIN, RCG25352, ISOFORM CRA_B; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: GORASP1, GRASP 65, RCG_25352; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PDZ DOMAIN, GOLGI STACKING PROTEIN, GOLGI, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.LIU,J.HU REVDAT 4 20-MAR-24 4KFV 1 REMARK LINK REVDAT 3 15-NOV-17 4KFV 1 REMARK REVDAT 2 22-JAN-14 4KFV 1 JRNL REVDAT 1 21-AUG-13 4KFV 0 JRNL AUTH Y.FENG,W.YU,X.LI,S.LIN,Y.ZHOU,J.HU,X.LIU JRNL TITL STRUCTURAL INSIGHT INTO GOLGI MEMBRANE STACKING BY GRASP65 JRNL TITL 2 AND GRASP55 PROTEINS JRNL REF J.BIOL.CHEM. V. 288 28418 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23940043 JRNL DOI 10.1074/JBC.M113.478024 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 9497 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 453 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.0670 - 3.1718 0.99 3139 143 0.2019 0.2483 REMARK 3 2 3.1718 - 2.5178 1.00 2992 162 0.2252 0.3117 REMARK 3 3 2.5178 - 2.2000 0.98 2913 148 0.2404 0.3401 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.32 REMARK 3 B_SOL : 22.99 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.60590 REMARK 3 B22 (A**2) : 0.44580 REMARK 3 B33 (A**2) : 2.16010 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1587 REMARK 3 ANGLE : 1.149 2150 REMARK 3 CHIRALITY : 0.084 229 REMARK 3 PLANARITY : 0.005 283 REMARK 3 DIHEDRAL : 17.372 582 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4KFV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079286. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9540 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS (PH 5.5) 25% PEG3350, REMARK 280 LIQUID DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 22.49450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.14350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.49450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.14350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 LEU A 3 REMARK 465 GLY A 4 REMARK 465 ALA A 5 REMARK 465 SER A 6 REMARK 465 SER A 7 REMARK 465 GLU A 8 REMARK 465 GLN A 9 REMARK 465 PRO A 10 REMARK 465 ALA A 11 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 33 O HOH A 453 1.89 REMARK 500 O HOH A 479 O HOH A 481 1.96 REMARK 500 O HOH A 484 O HOH A 493 2.13 REMARK 500 O HOH A 433 O HOH A 476 2.14 REMARK 500 NE ARG A 173 O HOH A 401 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 35 -52.49 68.78 REMARK 500 HIS A 44 -0.52 64.86 REMARK 500 LEU A 115 -127.67 -100.35 REMARK 500 TYR A 131 -21.19 73.31 REMARK 500 ASP A 139 23.96 -79.53 REMARK 500 LEU A 142 -81.05 -46.97 REMARK 500 GLN A 143 32.82 -152.40 REMARK 500 GLU A 144 2.66 -157.11 REMARK 500 SER A 145 29.82 -64.36 REMARK 500 GLU A 146 -114.15 -73.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 17 ND1 REMARK 620 2 HIS A 19 NE2 104.8 REMARK 620 3 CYS A 102 SG 122.4 110.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KFW RELATED DB: PDB DBREF 4KFV A 1 210 UNP B1WBR1 B1WBR1_RAT 1 210 SEQRES 1 A 210 MET GLY LEU GLY ALA SER SER GLU GLN PRO ALA GLY GLY SEQRES 2 A 210 GLU GLY PHE HIS LEU HIS GLY VAL GLN GLU ASN SER PRO SEQRES 3 A 210 ALA GLN GLN ALA GLY LEU GLU PRO TYR PHE ASP PHE ILE SEQRES 4 A 210 ILE THR ILE GLY HIS SER ARG LEU ASN LYS GLU ASN ASP SEQRES 5 A 210 THR LEU LYS ALA LEU LEU LYS ALA ASN VAL GLU LYS PRO SEQRES 6 A 210 VAL LYS LEU GLU VAL PHE ASN MET LYS THR MET ARG VAL SEQRES 7 A 210 ARG GLU VAL GLU VAL VAL PRO SER ASN MET TRP GLY GLY SEQRES 8 A 210 GLN GLY LEU LEU GLY ALA SER VAL ARG PHE CYS SER PHE SEQRES 9 A 210 ARG ARG ALA SER GLU HIS VAL TRP HIS VAL LEU ASP VAL SEQRES 10 A 210 GLU PRO SER SER PRO ALA ALA LEU ALA GLY LEU ARG PRO SEQRES 11 A 210 TYR THR ASP TYR ILE VAL GLY SER ASP GLN ILE LEU GLN SEQRES 12 A 210 GLU SER GLU ASP PHE PHE THR LEU ILE GLU SER HIS GLU SEQRES 13 A 210 GLY LYS PRO LEU LYS LEU MET VAL TYR ASN SER GLU SER SEQRES 14 A 210 ASP SER CYS ARG GLU VAL THR VAL THR PRO ASN ALA ALA SEQRES 15 A 210 TRP GLY GLY GLU GLY SER LEU GLY CYS GLY ILE GLY TYR SEQRES 16 A 210 GLY TYR LEU HIS ARG ILE PRO THR GLN PRO SER SER GLN SEQRES 17 A 210 TYR LYS HET ZN A 301 1 HET CL A 302 1 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 2 ZN ZN 2+ FORMUL 3 CL CL 1- FORMUL 4 HOH *97(H2 O) HELIX 1 1 SER A 25 ALA A 30 1 6 HELIX 2 2 ASP A 52 ASN A 61 1 10 HELIX 3 3 SER A 103 HIS A 110 1 8 HELIX 4 4 SER A 121 GLY A 127 1 7 HELIX 5 5 ASP A 147 HIS A 155 1 9 SHEET 1 A 4 SER A 45 ARG A 46 0 SHEET 2 A 4 ASP A 37 ILE A 42 -1 N ILE A 42 O SER A 45 SHEET 3 A 4 VAL A 66 ASN A 72 -1 O PHE A 71 N PHE A 38 SHEET 4 A 4 VAL A 78 VAL A 83 -1 O VAL A 81 N LEU A 68 SHEET 1 B 4 SER A 45 ARG A 46 0 SHEET 2 B 4 ASP A 37 ILE A 42 -1 N ILE A 42 O SER A 45 SHEET 3 B 4 PHE A 16 VAL A 21 -1 N PHE A 16 O ILE A 39 SHEET 4 B 4 ALA A 97 PHE A 101 -1 O ARG A 100 N HIS A 17 SHEET 1 C 5 SER A 171 VAL A 177 0 SHEET 2 C 5 LEU A 160 ASN A 166 -1 N LEU A 162 O VAL A 175 SHEET 3 C 5 ASP A 133 SER A 138 -1 N TYR A 134 O TYR A 165 SHEET 4 C 5 TRP A 112 VAL A 117 -1 N TRP A 112 O ILE A 135 SHEET 5 C 5 CYS A 191 GLY A 194 -1 O GLY A 194 N HIS A 113 LINK ND1 HIS A 17 ZN ZN A 301 1555 1555 2.35 LINK NE2 HIS A 19 ZN ZN A 301 1555 1555 2.34 LINK SG CYS A 102 ZN ZN A 301 1555 1555 2.48 CISPEP 1 GLY A 12 GLY A 13 0 4.53 CISPEP 2 TYR A 209 LYS A 210 0 -15.94 SITE 1 AC1 4 HIS A 17 HIS A 19 CYS A 102 CL A 302 SITE 1 AC2 3 HIS A 17 ALA A 107 ZN A 301 CRYST1 44.989 104.287 37.932 90.00 90.00 90.00 P 21 21 2 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.022228 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009589 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026363 0.00000